Evolution and Domestication of Core Eudicot Defense Mechanisms against a Common Generalist Pathogen

University Of California-Davis, Davis CA

Investigators

Abstract

Plant defense variation studies typically focus on single large effect genes within a host or specialist pathogen that interact only with each other. However, resistance to most generalist pathogens is quantitative and cannot be investigated using few genotypically distinct individuals. This project will begin one of the first direct surveys of how genomic diversity within and across core plant lineages may be shaped by genomic diversity in a broad spectrum generalist fungus that can infect most if not all plants. This will lead to the development of novel biological and statistical methods to handle genomic diversity across phylogenetic lineages and provide a unique multi-plant species dataset that is currently only feasible with Botrytis cincerea. All data and analysis protocols will be publicly available and microbial isolates will be available upon request pending the acquisition of the appropriate permits. With regard to training, the project will provide research opportunities for high school, undergraduate, and graduate students. These students will be trained in modern quantitative genetics of complex traits to prepare them for future careers in industry or academics. As this is the one of the first instances of attempting to do quantitative genetics in two interacting species, this will place them at the forefront of the field in both theory and computational applications. Undergraduates will develop and devise their own projects within the frame of this project. Any publication resulting from this research will likely include at least one undergraduate student as a co-author who was integral in designing and interpreting the experiments. In addition, the principal investigator will be involved in teaching, both in a university classroom setting and in ongoing outreach efforts to educate community members about plant metabolism, plant defense evolution, and quantitative genomics. Plant/pathogen interactions determine plants fitness/yield. Most research on plant/pathogen interactions focuses on epidemic diseases from pathogens that infect only one or a few species similar to the human flu. However, this has led to a paucity of research on pathogens that are endemic, like Botrytis cinerea or the common cold, which can infect most host genotypes but only cause a low level of economic loss. These generalist pathogens place evolutionary pressure across plant lineages, yet this cross-lineage pressure is rarely systematically addressed. For example, it is currently not known if there is a common plant defense network against these generalist pathogens that can function in all plants. To test this question, this project aims to: 1) measure lesion development with a high-throughput platform across six plant species that have independently undergone domestication (lettuce, tomato, grape, soy and Brassicas) with 100 genome sequenced isolates of the pathogen, Botrytis cinerea; 2) use the genome wide association mapping dataset to identify pathogenicity networks within the pathogen that allow it to infect these diverse hosts; 3) identify and validate plant gene targets of these networks using a new co-species co-expression network approach to test if the pathogen targets defense mechanisms that are conserved or variant across plants and if these defense mechanisms have been affected by human driven domestication; and 4) conduct transcriptome profiling across these plant/pathogen combinations to identify conserved or variant transcriptional responses across the eudicot lineages. By including domestic and wild genotypes in each plant species this project will provide a common reference frame in which to study how domestication may or may not consistently influence plant defenses. In the longer term, this information will provide for a better understanding of how selection pressures drive the evolution of defenses within eudicot lineages towards generalist pathogens.